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Implemented #144, partial volume via settings #145

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Jun 23, 2022
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Implemented #144, partial volume via settings #145

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bfcb118
Implemented #144, partial volume via settings
jnoelke Jun 1, 2022
cea6cd2
Adapt partial volume behaviour
jnoelke Jun 13, 2022
e63062f
Coding style
jnoelke Jun 15, 2022
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9 changes: 7 additions & 2 deletions simpa/core/device_digital_twins/pa_devices/ithera_msot_acuity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -145,14 +145,19 @@ def update_settings_for_use_of_model_based_volume_creator(self, global_settings)
structure_dict[Tags.STRUCTURE_END_MM][2] = structure_dict[Tags.STRUCTURE_END_MM][
2] + z_dim_position_shift_mm

if Tags.CONSIDER_PARTIAL_VOLUME_IN_DEVICE in volume_creator_settings:
consider_partial_volume = volume_creator_settings[Tags.CONSIDER_PARTIAL_VOLUME_IN_DEVICE]
else:
consider_partial_volume = False

if Tags.US_GEL in volume_creator_settings and volume_creator_settings[Tags.US_GEL]:
us_gel_layer_settings = Settings({
Tags.PRIORITY: 5,
Tags.STRUCTURE_START_MM: [0, 0,
heavy_water_layer_height_mm + mediprene_layer_height_mm],
Tags.STRUCTURE_END_MM: [0, 0,
heavy_water_layer_height_mm + mediprene_layer_height_mm + us_gel_thickness],
Tags.CONSIDER_PARTIAL_VOLUME: True,
Tags.CONSIDER_PARTIAL_VOLUME: consider_partial_volume,
Tags.MOLECULE_COMPOSITION: TISSUE_LIBRARY.ultrasound_gel(),
Tags.STRUCTURE_TYPE: Tags.HORIZONTAL_LAYER_STRUCTURE
})
Expand All @@ -163,7 +168,7 @@ def update_settings_for_use_of_model_based_volume_creator(self, global_settings)
Tags.PRIORITY: 5,
Tags.STRUCTURE_START_MM: [0, 0, heavy_water_layer_height_mm],
Tags.STRUCTURE_END_MM: [0, 0, heavy_water_layer_height_mm + mediprene_layer_height_mm],
Tags.CONSIDER_PARTIAL_VOLUME: True,
Tags.CONSIDER_PARTIAL_VOLUME: consider_partial_volume,
Tags.MOLECULE_COMPOSITION: TISSUE_LIBRARY.mediprene(),
Tags.STRUCTURE_TYPE: Tags.HORIZONTAL_LAYER_STRUCTURE
})
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4 changes: 3 additions & 1 deletion simpa/utils/libraries/structure_library/StructureBase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,9 @@ def __init__(self, global_settings: Settings,
if Tags.PRIORITY in single_structure_settings:
self.priority = single_structure_settings[Tags.PRIORITY]

self.partial_volume = single_structure_settings[Tags.CONSIDER_PARTIAL_VOLUME]
if Tags.CONSIDER_PARTIAL_VOLUME in single_structure_settings:
self.partial_volume = single_structure_settings[Tags.CONSIDER_PARTIAL_VOLUME]
else: self.partial_volume = False
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I think our coding convention is to have if else block statements on a new line unless it is an inline if-else. Apart from that the changes look reasonable.

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Alright, I changed this.


self.molecule_composition = single_structure_settings[Tags.MOLECULE_COMPOSITION]
self.molecule_composition.update_internal_properties()
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6 changes: 6 additions & 0 deletions simpa/utils/tags.py
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Expand Up @@ -191,6 +191,12 @@ class Tags:
If True, the structure will be generated with its edges only occupying a partial volume of the voxel.\n
Usage: adapter versatile_volume_creation
"""
CONSIDER_PARTIAL_VOLUME_IN_DEVICE = ("consider_partial_volume_in_device", bool)
"""
If True, the structures inside the device (i.e. US gel and membrane) will be generated with its edges
only occupying a partial volume of the voxel. \n
Usage: adapter versatile_volume_creation
"""

STRUCTURE_START_MM = ("structure_start", (list, tuple, np.ndarray))
"""
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